1ZPK

Crystal structure of the complex of mutant HIV-1 protease (A71V, V82T, I84V) with a hydroxyethylamine peptidomimetic inhibitor BOC-PHE-PSI[R-CH(OH)CH2NH]-PHE-GLU-PHE-NH2

Structural Biology Knowledgebase: 1ZPK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.156

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1ZPK

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 22554.28

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEASE RETROPEPSIN A, B 99 Human immunodeficiency virus 1 EC#: 3.4.23.16 IUBMB
Mutation: A71V, V82T, I84V
Gene Name(s): gag-pol pol

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0ZS
Query on 0ZS

A N-{(2R,3S)-3-[(tert-butoxycarbonyl)amino]- 2-hydroxy-4-phenylbutyl}-L-phenylalanyl-L- alpha-glutamyl-L-phenylalaninamide
C38 H49 N5 O8
MPMUDVMRFYJRLP-QEUNAIBPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000385 (PHE,T00,GLU,NH2,BOC) A BOC-PHE-PSI[R-CH(OH)CH2NH]-PHE-GLU-PHE-NH2 Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
A, B L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.156
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 62.48 α = 90.00
b = 62.48 β = 90.00
c = 82.41 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-05-17
  • Released Date: 2006-04-25
  • Deposition author(s): Duskova, J., Skalova, T., Dohnalek, J., Petrokova, H., Hasek, J.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature